Ionic environment effects on the dynamics of biomolecular assemblies

Ions play an essential role in biomolecular assemblies and catalytic reactions. Particularly, the concentration of monovalent (e.g. K+, Cl-) and divalent (e.g. Mg2+) ions can significantly affect the dynamics and the stability of the tertiary structure of RNA. To understand the precise ways by which ionic interactions control the energetics and dynamics of RNA, we are extending a class of simplied models, called all-atom structure-based model (SMOG), that include effects of diffuse monovalent and divalent ions. In contrast to our earlier studies, this model is able to capture the crucial effects of the inner-shell interactions, in addition to more diffuse ions. These extensions require an accurate parametrization to model the precise coordination distances and geometries between ions and phosphate groups, in addition to the relative energetics of inner-shell and outer-shell interactions. Calibration of the model has been performed through comparisons with highly-detailed explicit-solvent models and titration experiments. As a benchmark, the model can accurately predict the number of excess Mg2+ ions for RNA systems (e.g. 58-mer, adenine-riboswitch) over a range of concentrations, which have been measured experimentally. With this foundation, we are now able to study the effects of the ionic environment on large-scale rearrangement of ribonucleoprotein assemblies, such as the ribosome.